did you accidentally trip lyall so he planted the flower in the gardens?
no, tackling is the way to go to speed up his route faster. Lyall’s route is a bit more time specific however certain events have to be triggered before the main plot progressed. His second date triggers after the jellyfish event is done, and cannot be triggered after Leynar tells you about their missing children problem (when Ignia starts meddling with the island, you can check the orphanage and whatnot)
Basically you have to trigger the second date around the time you r dealing with Io